update code format

phipsonlab · Sep 10, 2024 · 45fc9ee · 45fc9ee
1 parent d2dff1d
commit 45fc9ee
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Showing 11 changed files with 40 additions and 19 deletions.
diff --git a/R/create_genesets.R b/R/create_genesets.R
@@ -53,8 +53,8 @@ check_geneset_input <- function(data_lst, bin_type, bin_param,
 
     use_cm <- FALSE
     for (i in names(data_lst)){
-        rpp = data_lst[[i]]
-        if (class(rpp) == "list"){
+        rpp <- data_lst[[i]]
+        if (is(rpp,"list")){
             req_cols <- c('x', 'y', 'feature_name' )
             if (length(setdiff(req_cols, colnames(rpp$trans_info))) > 0){
                 stop("Invalid column names detected in input data_lst. 

diff --git a/R/get_vectors.R b/R/get_vectors.R
@@ -432,7 +432,7 @@ get_vectors<- function(data_lst, cluster_info,cm_lst=NULL, bin_type, bin_param,
             stop("Invalid input all_genes, should be a vector of character")}
         req_cols <- c("x", "y","feature_name")
         for (i in names(data_lst)){
-            rpp = data_lst[[i]]
+            rpp <- data_lst[[i]]
             if (length(setdiff(req_cols, colnames(rpp$trans_info))) > 0)
                 stop("Invalid column names detected in input data_lst.
                         Must contain columns 'x', 'y',

diff --git a/R/jazzpanda-package.R b/R/jazzpanda-package.R
@@ -10,7 +10,9 @@
 #' }
 #' @usage data(rep1_sub)
 #' @return List
-#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep1/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip}
+#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/\allowbreak 
+#' Xenium_FFPE_Human_Breast_Cancer_Rep1/Xenium_FFPE_Human_Breast\allowbreak
+#' _Cancer_Rep1_outs.zip}
 "rep1_sub"
 
 
@@ -30,7 +32,9 @@
 #' }
 #' @usage data(rep1_clusters)
 #' @return  data frame
-#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep1/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip}
+#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/\allowbreak
+#' Xenium_FFPE_Human_Breast_Cancer_Rep1/Xenium_FFPE_Human_Breast_\allowbreak
+#' Cancer_Rep1_outs.zip}
 "rep1_clusters"
 
 #' Rep1 negative control genes within the selected region.
@@ -47,7 +51,9 @@
 #' }
 #' @usage data(rep1_neg)
 #' @return List
-#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep1/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip}
+#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/\allowbreak
+#' Xenium_FFPE_Human_Breast_Cancer_Rep1/Xenium_FFPE_Human_Breast_\allowbreak
+#' Cancer_Rep1_outs.zip}
 "rep1_neg"
 
 
@@ -63,7 +69,9 @@
 #' }
 #' @usage data(rep2_sub)
 #' @return List
-#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep2/Xenium_FFPE_Human_Breast_Cancer_Rep2_outs.zip}
+#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/\allowbreak
+#' Xenium_FFPE_Human_Breast_Cancer_Rep2/Xenium_FFPE_Human_Breast_\allowbreak
+#' Cancer_Rep2_outs.zip}
 "rep2_sub"
 
 
@@ -83,7 +91,9 @@
 #' }
 #' @usage data(rep2_clusters)
 #' @return  data frame
-#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep2/Xenium_FFPE_Human_Breast_Cancer_Rep2_outs.zip}
+#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/\allowbreak
+#' Xenium_FFPE_Human_Breast_Cancer_Rep2/Xenium_FFPE_Human_\allowbreak
+#' Breast_Cancer_Rep2_outs.zip}
 "rep2_clusters"
 
 #' Rep2 negative control genes within the selected region.
@@ -100,5 +110,7 @@
 #' }
 #' @usage data(rep2_neg)
 #' @return List
-#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep2/Xenium_FFPE_Human_Breast_Cancer_Rep2_outs.zip}
+#' @source \url{https://cf.10xgenomics.com/samples/xenium/1.0.1/\allowbreak
+#' Xenium_FFPE_Human_Breast_Cancer_Rep2/Xenium_FFPE_Human_Breast_\allowbreak
+#' Cancer_Rep2_outs.zip}
 "rep2_neg"
diff --git a/R/lasso_markers.R b/R/lasso_markers.R
@@ -39,7 +39,7 @@ check_valid_input<- function(gene_mt,cluster_mt,sample_names, n_fold=10,
         if (any(!non_numeric_cols)) {
             stop("Column names for cluster_mt contain integers.")
         }
-     })
+    })
     if (nrow(gene_mt) != nrow(cluster_mt)){
         stop("Number of rows of gene_mt and cluster_mt does not match.") }
     # every gene should have non-zero variance

diff --git a/inst/script/generate_vignette_data.R b/inst/script/generate_vignette_data.R
@@ -31,7 +31,6 @@
 library(data.table)
 library(Seurat)
 # download the official cell types of both samples
-# Specify the URL of the file
 s1_url <- "https://raw.githubusercontent.com/phipsonlab/jazzPanda_vignette/main/Xenium_rep1_supervised_celltype.csv"
 s2_url <- "https://raw.githubusercontent.com/phipsonlab/jazzPanda_vignette/main/Xenium_rep2_supervised_celltype.csv"
 # Download the file
@@ -69,7 +68,6 @@ get_xenium_data<-function(path,mtx_name, trans_name="transcript_info.csv.gz",
 }
 
 rep1_path <- 'path/to/rep1/out/directory'
-rep1_path="/stornext/Bioinf/data/lab_phipson/data/xenium_human_breast_cancer/rep1/"
 rep1 = get_xenium_data(rep1_path,
                 mtx_name="cell_feature_matrix",
                 trans_name="transcripts.csv.gz",
@@ -181,7 +179,6 @@ rep1_neg = list(trans_info=trans_neg,
 
 # process the rep2 in the same way
 rep2_path <- 'path/to/rep2/out/directory'
-rep2_path="/stornext/Bioinf/data/lab_phipson/data/xenium_human_breast_cancer/rep2/"
 rep2 = get_xenium_data(rep2_path,
                 mtx_name="cell_feature_matrix",
                 trans_name="transcripts.csv.gz",

diff --git a/man/rep1_clusters.Rd b/man/rep1_clusters.Rd
diff --git a/man/rep1_neg.Rd b/man/rep1_neg.Rd
diff --git a/man/rep1_sub.Rd b/man/rep1_sub.Rd
diff --git a/man/rep2_clusters.Rd b/man/rep2_clusters.Rd
diff --git a/man/rep2_neg.Rd b/man/rep2_neg.Rd
diff --git a/man/rep2_sub.Rd b/man/rep2_sub.Rd